sirselim
Senior Bioinformatician | Applications | @nanoporetech - passionate about science, technology, community empowerment, photography and heavy metal.
@nanoporetechTaranaki, New Zealand
Pinned Repositories
diagnostics_exome_reporting
Pipeline to filter whole exome vcf files and generate a report document for clinical diagnostics.
guppy_parameter_optimiser
A small bash script that automates sweeping Guppy parameters in an attempt to optimise basecalling rate
illumina450k_filtering
A collection of resources to filter 'bad' probes from the Illumina 450k and EPIC methylation arrays
Intro_to_GWAS
An introductory workshop to GWAS analysis using PLINK and R
jetson_nanopore_sequencing
A place to collate notes and resources of our journey into porting nanopore sequencing over to accessible, portable technology.
methylation_EWAS_workshop
This is a basic EWAS tutorial, introducing basic concepts for analysing methylation data
WES_ShinyDiscover
A Shiny interface to filter and identify variants of interest from whole exome data
sirselim's Repositories
sirselim/jetson_nanopore_sequencing
A place to collate notes and resources of our journey into porting nanopore sequencing over to accessible, portable technology.
sirselim/guppy_parameter_optimiser
A small bash script that automates sweeping Guppy parameters in an attempt to optimise basecalling rate
sirselim/illumina450k_filtering
A collection of resources to filter 'bad' probes from the Illumina 450k and EPIC methylation arrays
sirselim/GPU-musings
A collection of my thoughts around GPUs for genomic analysis and sequencing
sirselim/presentation_and_design_resources
A small repo to hold useful resources for various courses I teach
sirselim/sirselim.github.io
Personal website, blog and notebook
sirselim/tSNE_plotting
some documentation for exploring the plotting of tSNE results from various data sources
sirselim/singularity-genmod
A quick singularity recipe for genmod to facilitate use in variant annotation pipelines
sirselim/immunecell_methylation_paper_data
This repository contains data, results and supplementary information to go alongside our manuscript detailing the validation of immune cell specific methylation markers.
sirselim/mitofish
This script generates "baited" sequences from across a provided reference to search for them in fastq file(s)
sirselim/MTG-Markdown-Generator
A Python script to generate markdown tables for Magic: The Gathering cards using the Scryfall API.
sirselim/MTGCardFinder
MTG Card Markdown Toolkit - a VSCode extension to grab card image and information for markdown documents.
sirselim/NvidiaGTC_2021
My 40min presentation for Nvidia Spring GTC 2021 on portable sequencing tech and Nvidia GPUs
sirselim/sirselim
sirselim/smrnaseq
A small-RNA sequencing analysis pipeline
sirselim/bootNet
bootNet is a wrapper for the fantastic glmnet function - it brings bootstrapping and parallel processing to the elastic-net framework.
sirselim/covid_analysis
Exploration of new Zealand COVID19 data from the MoH
sirselim/AlkResBaz_KeyStory_2020
My Key Story presentation for Auckland Research Bazaar 2020
sirselim/amr
amr_finder
sirselim/bedmeth2bedgraph
Small tool to convert bedmethyl format to custom bedgraph output
sirselim/CLNR_401_plenary_presentation
My plenary presentation for the CLNR 401 weekend seminar
sirselim/CMDHB-Visit-Jan2021
Short presention on portable sequencing for CMDHB visit to ESR
sirselim/eResearch-Presentation-2021
My eResearch 2021 presentation on portable sequencing technology and it's role in community driven science.
sirselim/frontline_genomics_presentation
Our presentation on 'real-time' genomics for ESR Data Science Week 2020.
sirselim/Miles_CV
An online repository to provide an updated personal and professional CV.
sirselim/presentation_karaoke
1 minute, random topic, random slides --- GO!
sirselim/presentation_maps
A repo to store maps used in my presentations
sirselim/random_plotting_scripts
A dump of some random and testing plotting scripts from various languages
sirselim/spotify-github-profile
Show your Spotify playing on your Github profile
sirselim/streamlit_app_test
A small repo to test out streamlit, a new tool for serving awesome web-based python apps.